$10 buck thermocycler design work

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Bryan Bishop

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Feb 5, 2009, 7:12:38 PM2/5/09
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Hey all,

Tito and I were just talking a few minutes ago about the $10
thermocycler. I know that Joseph Jackson is working on commercializing
it, but the DIY crowd can bypass the patents and just go make it. What
we need at the moment is for a few people to read through the paper,
make some notes on the design, post the notes on the design, and then
come up with some arbitrary schedule for the project in terms of
milestones. I wouldn't mind contributing to the design.

$10 thermocycler paper-
http://heybryan.org/~bbishop/docs/thermocycler.pdf

I'll be sure to post some notes of my own in a while, but I will
readily admit that my electronics skill has been rusty, now that I can
hardly sneak a soldering iron into my dorm. ;-)

- Bryan
http://heybryan.org/
1 512 203 0507

George Xu

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Feb 5, 2009, 8:47:48 PM2/5/09
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Hi all,

I've taken a brief look at the paper and the supporting info PDF (attached) which pretty much lays out the design, including the circuit. I'm not sure how they kept the cost under $10 if they use a cartridge resistance heater (browsing omega's site seems to indicate that cartridge heaters are relatively expensive). It seems that NiChrome wire would be a much cheaper alternative.

On a semi-related note, does anyone know anything about doing PCR with microfluidics? A while back there was an article about making general microfluidics devices using Shrinky-Dinks (http://www.labplusinternational.com/index.php?id=2155) that sounds very DIY-able. 

George
Mini PCR Machine - Supporting Info.PDF

JonathanCline

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Feb 6, 2009, 1:25:43 AM2/6/09
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On Feb 5, 7:47 pm, George Xu <x.geo...@gmail.com> wrote:
> Hi all,
>
> I've taken a brief look at the paper and the supporting info PDF (attached)
> which pretty much lays out the design, including the circuit.
> ...
> On a semi-related note, does anyone know anything about doing PCR with
> microfluidics? A while back there was an article about making general
> microfluidics devices using Shrinky-Dinks (http://www.labplusinternational.com/index.php?id=2155) that sounds very
> DIY-able.
>
> George
>

There is a very interesting summary and comparison of methods in this
ref below. Regarding the patent issue on the "$10 thermocycler", I
have to wonder how easy it would be to work around the patent (I
haven't read it). I would also like to try the shrinky-dinks at some
point - I saw the chip fabrication required a vacuum chamber (to
remove bubbles), so I'd have to get tooled first.

Miniaturized PCR chips for nucleic acid amplification and analysis:
latest advances and future trends
Chunsun Zhang and Da Xing
Nucleic Acids Res. 2007 July; 35(13): 4223–4237.
Published online 2007 June 18. doi: 10.1093/nar/gkm389.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17576684

## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

Cory Tobin

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Feb 6, 2009, 3:03:35 AM2/6/09
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> On a semi-related note, does anyone know anything about doing PCR with
> microfluidics?

You would only want to do microfluidic-PCR if your specific project
required very small volumes. For general purposes I would stick to
"regular PCR" (20-50uL). The microfluidic platform just adds an
unnecessary level of complexity to something that is fairly simple.

But if you're actually interested in microfluidics, then by all means go for it!


> A while back there was an article about making general
> microfluidics devices using Shrinky-Dinks
> (http://www.labplusinternational.com/index.php?id=2155) that sounds very
> DIY-able.

When that paper first came out I tried it out in my lab. I didn't get
very good results. The main problem was that the shrinky material
didn't shrink uniformly. I tried a number of different ovens around
campus, including some convection ovens (recommended by the authors),
but the channels always ended up warped. I'm not sure if the problem
was due to the material or just uneven heating. Other people may have
improved on the technique since the original publication. If you're
interested in the shrinky-dink-microfluidics you may want to browse
the journal "Lab on a Chip" for more recent protocols.


-Cory

Gene Hacker

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Feb 19, 2009, 5:14:35 PM2/19/09
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How about using a big resistor for the heating element? Resistors are
more readily available than insulated nichrome wire. Though,
uninsulated nichrome wire is for the most part very easy to obtain
from broken hair dryers. One might also be able to make all the metal
parts, including the thermal interconnects, from laser cut metal from
Ponoko. Where can one obtain small diameter tubing though?

Marnia Johnston

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Feb 19, 2009, 5:56:05 PM2/19/09
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I get my NiChrom wire from ceramic/art supply stores....
PS: I have vacuum chamber making materials for the Bay Area people...
-Marnia
 

Nick Taylor

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Feb 19, 2009, 8:09:28 PM2/19/09
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> How about using a big resistor for the heating element? Resistors are
> more readily available than insulated nichrome wire. Though,
> uninsulated nichrome wire is for the most part very easy to obtain
> from broken hair dryers. One might also be able to make all the metal
> parts, including the thermal interconnects, from laser cut metal from
> Ponoko. Where can one obtain small diameter tubing though?


I've had a bit of a play with Ponoko recently - you'll instantly blow your $10 budget on postage alone.

I'm a kiwi so I feel some vague twinges of loyalty etc, but really, if they don't sort out their material costs, their turnaround time and their postage costs, they're going to be completely blind-sided by EU/US operators who do.

As far as laser-cutting goes, you might be better off befriending your local laser-cutting place - although I haven't actually tried this myself yet so don't know if they have mega setup-charges etc.

Alternatively if 30-50 of us punt $100 each, we could buy our own and use our own recycled open-sourced packaging etc, which the open-manufacturing lot are quite keen on developing.


This list is great btw. Every day a couple of things turn up that make me go "holy crap!"

Bryan Bishop

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Feb 19, 2009, 8:34:07 PM2/19/09
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On Thu, Feb 19, 2009 at 7:09 PM, Nick Taylor wrote:
> This list is great btw. Every day a couple of things turn up that make me go
> "holy crap!"

http://heybryan.org/~bbishop/docs/diybio.png (warning: obscenities)

That about sums it up, Nick.

IronGhost

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Sep 12, 2011, 1:00:53 AM9/12/11
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How about a surplus Peltier Device from a CPU cooler, they can heat or cool, depending on how you hook them up, hacking the alarm output on a simple digital timer with a transistor switch and a relay to flip the polarity could be used to switch between heat and cool modes.

Nathan McCorkle

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Sep 12, 2011, 9:50:12 AM9/12/11
to diy...@googlegroups.com, Bryan Bishop
On Thu, Feb 19, 2009 at 8:34 PM, Bryan Bishop <kan...@gmail.com> wrote:
>
> On Thu, Feb 19, 2009 at 7:09 PM, Nick Taylor wrote:
>> This list is great btw. Every day a couple of things turn up that make me go
>> "holy crap!"
>
> http://heybryan.org/~bbishop/docs/diybio.png (warning: obscenities)

link is down

>
> That about sums it up, Nick.
>
> - Bryan
> http://heybryan.org/
> 1 512 203 0507
>

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Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

Dakota Hamill

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Sep 12, 2011, 11:10:05 AM9/12/11
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I've been reading up on just that thing the past couple of days. 

http://tomswiki.wetpaint.com/page/Peltier+%28TEC%29+Cooling

http://www.heatsink-guide.com/peltier.htm


The nice thing about them, as you mentioned, is that you could reverse the polarity on one cooler, thus switching the "hot" and "cold" sides, although you need a way to move the heat off of one side to maintain the temperature gradient.  Even a low wattage one I'm sure would give you pretty decent ramp times, as heating 200 micro-liters 0.200 mL in your average PCR tube only needs ~ 58J to go from room temp to 95C.

They are pretty cheap online too, $5 to $10 which could warrant messing around with them and taking temperature readings.  I imagine you'd need a decent power supply though for the current they draw.

http://www.amazon.com/TEC1-12706-Thermoelectric-Peltier-Cooler-Volt/dp/B002UQQ3Q2

I searched instructables and really liked these peoples design

http://www.instructables.com/id/Coffee-Cup-PCR-Thermocycler-costing-under-350/

nice solid little aluminum block and a little $20 heater plug that goes into the center.  The reason it cost $350 was that the Electrical Temperature Controller thingy they used was $300+!!!  That is something that I am almost sure can be replaced by something cheaper.






John Griessen

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Sep 12, 2011, 2:07:23 PM9/12/11
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On 09/12/2011 10:10 AM, Dakota Hamill wrote:
> although you need a way to move the heat off of one side to maintain the temperature gradient.

The thermal mass of TE coolers needs considering. Running them dumps heat right into them, so switching
involves delay while the heat flows. The hot side heat needs to all go some where before
that spot can be cool. I like the idea of running the coolers steady state and
flipping open different doors to allow air flow past them or past heaters or ambient
to rapidly change heat flow to or from samples in heat finned vials surrounded by
flowing air. Small door flippers can be made from plastic piezo electric film actuator material
that is inexpensive and fairly low power consumption, (think battery operation, solar cell operation, or just
low waste heat generation in your room)

John

Kaustubh

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Sep 13, 2011, 1:22:07 PM9/13/11
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Hi everyone,
I can't top the $10 PCR, but here's our attempt at creating a <$500
model. I know there are a lot of DIY thermal cyclers around, but
there's always room for more.
Besides, ours is the only one I know of that has a clear polycarbonate
enclosure :)

Pictures, report and a blog piece here:

http://abe-bhaleraolab.age.uiuc.edu/blog/2011/sep/13/diy-thermal-cycler/

Feel free to leave comments on the blog if you need specific
information.

Kaustubh

Matt Conway

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Sep 14, 2011, 1:43:47 AM9/14/11
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While the link shows TE coolers, there are multiple designs in the
paper, and the very exciting $10 design doesn't use TE coolers at
all.

For the sake of the original poster, here's my notes/take on the $10
pocket PCR machine. It consists of three aluminum blocks...looks to
be machined from 1 10mm x 8 mm block (8$ for 6 ft on McMasterCarr)
which are thermally connected by screws of different sizes and
materials..the temperature of the warmest block (denaturing) is
maintained by a thermistor/heater circuit, and the heat is transferred
to the second warmest block (extension) through stainless steel
screws, finally plastic screws connect the extension block to the
annealing block. Because the heat conducted through the screws would
be much greater than by any convective transfer between the blocks the
temperature of the annealing and extension blocks is fine tuned by the
size and material of the screws used. (To me this is the most
brilliant part of the design) The circuit for controlling the
temperature of the denaturing block is very simple and I haven't
double checked but $6 for the electrical parts seems right. It could
easily be soldered to a simple general purpose project board, and we
wouldn't need to make PCBs. The tubing seems like it wouldn't be too
expensive, and one of these blocks lends itself to parallel
processing. (Although this is mentioned in the paper)

Disadvantages to this design: (very few)
-Machining of Aluminum: (Only in the DIYbio context, I'm sure this
lends itself fine to mass production) I'm not an expert here or
anything, but any metal manipulations I've tried to do at home have
never ended well.
-Requires external thermocouple (and patience!) for calibration:
These aren't cheap, but are generally useful to have around. (Maybe
you can borrow your mom's digital meat thermometer)
-The idea of PCR in a circular tube is a bit of a paradigm shift and
does not play well with other high-throughput liquid handling tech
(yet?) but it's crude enough that we can all amplify anything we want
to at home.

TL;DR The $10 pocket PCR design could be adapted by us if we put our
heads together. The $10 dollar claim is a little extreme but it's
easily sub $30 factoring in shipping if you have a soldering iron,
wire, a way to machine aluminum and a thermocouple already. If
someone has a way to machine the blocks, I'd gladly trade a soldered
circuit, or maybe we can put our heads together and think of
premanufactured parts that could serve the role of the aluminum
block.

-Matt Conway
B.S. Chemical Engineering '12
University of Maryland
mfco...@umd.edu

Matt Conway

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Sep 14, 2011, 2:49:59 AM9/14/11
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Kaustubh said:
> I can't top the $10 PCR, but here's our attempt at creating a <$500
> model. I know there are a lot of DIY thermal cyclers around, but
> there's always room for more.
> Besides, ours is the only one I know of that has a clear polycarbonate
> enclosure :)

Very nice!

On Feb 5 2009, 8:12 pm, Bryan Bishop <kanz...@gmail.com> wrote:
> What we need at the moment is for a few people to read through the paper,
> make some notes on the design, post the notes on the design, and then
> come up with some arbitrary schedule for the project in terms of
> milestones.

Sorry to be a newcomer...Did you guys come up with any progress here?

The recent discussion is on peltier devices, which while they are
exciting, if you go back and look at the posted pdf, the $10 pocket
thermocycler achieves the correct temperatures in the three zones
without one. (Adding peltier devices make it the $100 thermocycler
easy) The trick is to separate the three aluminum blocks such that
they are connected only by the screws. This way the size of the screw
and how far its screwed in allow the user to calibrate the temperature
of the two cooler blocks assuming the hot blocks temperature is
constant. (Which it is! Due to the simple elegant circuit in the
data)

In terms of a DIYbio project,a huge difficulty lies in the fabrication
of the three aluminum blocks...Does anyone have any ideas or tools to
cut those aluminum blocks...I'll think about other objects that are
prefabbed to the right shape...


Matt Conway

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Sep 14, 2011, 2:51:35 AM9/14/11
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Oops! Sorry of the double post...thought the first one didn't go
through...

John Griessen

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Sep 14, 2011, 9:26:06 AM9/14/11
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On 09/14/2011 12:43 AM, Matt Conway wrote:
> -The idea of PCR in a circular tube is a bit of a paradigm shift and
> does not play well with other high-throughput liquid handling tech
> (yet?) but it's crude enough that

I don't see how a price of approx. $20 will be any more helpful for DIYbio
budgets than one that is $80 with time saving conveniences like thermocycling
12 samples at once, not having to super clean the special shaped tube
in place in the machine or re-thread a new one in after running a PCR on just one sample.
The TX A&M design with triangular tube path does have very low power consumption
good for battery operation, but I can easily see a machine based on air heat transfer
to vials having low enough power consumption to run on a small solar cell for
jungle/remote field applications. Plus the TX A&M design is a patented process, so
not available to produce even in kit form, where classic PCR can be DIY low cost/easy
and manufactured as an open hardware kit you don't have to hack bits of metal to get.

John

Nathan McCorkle

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Sep 14, 2011, 10:38:31 AM9/14/11
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I would say calibration is a big disadvantage.... what happens if a
guy down the hall/street in a different lab wants to borrow your PCR
machine, and he happens to have a window or Air Conditioner raising or
lowering his lab's temp. I wouldn't want to have to readjust screws
and stuff like that all the time. What about if I'm doing a PCR run,
and the central air conditioning turns on...

Unless ambient temp had a linear effect on all three heating
blocks/areas, this design suffers significantly in that area.

>
> TL;DR The $10 pocket PCR design could be adapted by us if we put our
> heads together.  The $10 dollar claim is a little extreme but it's
> easily sub $30 factoring in shipping if you have a soldering iron,
> wire, a way to machine aluminum and a thermocouple already.  If
> someone has a way to machine the blocks, I'd gladly trade a soldered
> circuit, or maybe we can put our heads together and think of
> premanufactured parts that could serve the role of the aluminum
> block.
>
> -Matt Conway
> B.S. Chemical Engineering '12
> University of Maryland
> mfco...@umd.edu
>
>
>
> On Sep 12, 2:07 pm, John Griessen <j...@industromatic.com> wrote:
>> On 09/12/2011 10:10 AM, Dakota Hamill wrote:
>>
>> > although you need a way to move the heat off of one side to maintain the temperature gradient.
>>
>> The thermal mass of TE coolers needs considering.  Running them dumps heat right into them, so switching
>> involves delay while the heat flows.  The hot side heat needs to all go some where before
>> that spot can be cool.  I like the idea of running the coolers steady state and
>> flipping open different doors to allow air flow past them or past heaters or ambient
>> to rapidly change heat flow to or from samples in heat finned vials surrounded by
>> flowing air.  Small door flippers can be made from plastic piezo electric film actuator material
>> that is inexpensive and fairly low power consumption, (think battery operation, solar cell operation, or just
>> low waste heat generation in your room)
>>
>> John
>

> --


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Simon Quellen Field

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Sep 14, 2011, 12:46:10 PM9/14/11
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Newton's Law of Cooling comes into play, making the difference between
office temperatures much less of a concern. When the temperature of the
device is well above the ambient temperature, small differences in the
ambient will have even smaller differences in the cooling rate.

But for $10 you can do the experiment.

How critical is calibration anyway? The nature of PCR suggests to me that
as long as the temperature cycles between hot enough and cold enough,
you should get amplification just fine. You don't want to cook the sample,
but other than that, do you care if it gets a little warmer than the last time?
Getting colder would seem to be a non-issue.

PCR experts -- how critical are the temperatures, and why?

-----
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Nathan McCorkle

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Sep 14, 2011, 1:44:27 PM9/14/11
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On Wed, Sep 14, 2011 at 12:46 PM, Simon Quellen Field
<sfi...@scitoys.com> wrote:
> Newton's Law of Cooling comes into play, making the difference between
> office temperatures much less of a concern. When the temperature of the
> device is well above the ambient temperature, small differences in the
> ambient will have even smaller differences in the cooling rate.
> But for $10 you can do the experiment.
> How critical is calibration anyway? The nature of PCR suggests to me that
> as long as the temperature cycles between hot enough and cold enough,
> you should get amplification just fine. You don't want to cook the sample,
> but other than that, do you care if it gets a little warmer than the last
> time?
> Getting colder would seem to be a non-issue.
> PCR experts -- how critical are the temperatures, and why?

I'm no expert, but I tried to amplify a piece of mRNA and didn't get
what I wanted. I'm going to try again by adjusting the annealing temp
a few degrees colder, then I'll try adjusting the Mg2+ concentration.

A few degrees can make the difference between specific and
non-specific binding. In the above case, I added linker regions to the
ends of my primers, so they're not completely specific. Decreasing the
temp a few degrees could prevent the non-specific regions from
dissociating the whole primer, and getting me the sequence that I want
to avoid getting synthesized.

John Griessen

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Sep 14, 2011, 1:49:05 PM9/14/11
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On 09/14/2011 12:43 AM, Matt Conway wrote:
> I'd gladly trade a soldered
>> circuit, or maybe we can put our heads together and think of
>> premanufactured parts

How about using CAD such as HeeksCAD to design some parts that can be cut out inexpensively?
Pre-made parts for something else will always be crude hacks stuck together with JB-Weld and
not very pretty, not anything that can be made inexpensively as a full assembly, just a
penny pinching hobbyist kludge.

How about using our heads to come up with a moderately priced path to a < $100
thermal cycler system made mostly of flat parts so they can be sent
around to different developers and testers by low cost first class mail?
I'm thinking of mechanical parts that fit together with press-on fit, screws,
silicone caulk. No sawing, drilling or measuring to assemble a kit.

I use HeeksCAD on linux, the main developers run it on windows, and it can probably
run on OS-X with a little effort.
I can spend small slivers of time to help others get up to speed for making things. Who's interested?

JG

Cathal Garvey

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Sep 14, 2011, 3:13:54 PM9/14/11
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In an ideal PCR, temperature can be pretty flakey. Sadly, all too often you need to optimise your sharpen bands or to get bands at all, and a well defined temperature profile can be critical.
The main issue addressed is non-specific binding, including primer dimers. However, primer hairpins and complex DNA (i.e. Secondary structures) can benefit from tightly controlled annealing conditions too.

So, depends: if you're doing off-the-shelf reactions designed for bush conditions, maybe not. Research or Development conditions, probably you do need good accuracy.

Jonathan Cline

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Sep 14, 2011, 3:23:11 PM9/14/11
to DIYbio, jcline
On Sep 14, 9:46 am, Simon Quellen Field <sfi...@scitoys.com> wrote:
>
> PCR experts -- how critical are the temperatures, and why?

I am not a PCR expert however feedback I've received is that
accuracy of +/- 2 degrees C is OK in most cases.

Being precise is far more important, so that the biologist
can count on the device to reproduce the same output
across many runs over many months, for comparison against
prior experimental data and/or controls.


The hybrid peltier/lava-amp approach would couple the mechanical
heat exchange (screws) with electronic controls. i.e. mount a
threaded rod to a servo and control the servo (thus heat exchange)
in real time by monitoring the thermocoupler.


I haven't looked at the bill of materials for openpcr yet I have
to believe that the cost can be cut in half - easily. This is based
on the off-the-shelf-modular-kit-based approach to the unit,
physical size, etc. So a great project would be to take the
currently working and well designed openpcr design and
branch it to make an openpcr-mini design. That's the
benefit of open licensing! We can all thank Tito for that.


--

Patrik

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Sep 14, 2011, 3:48:42 PM9/14/11
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> For the sake of the original poster, here's my notes/take on the $10
> pocket PCR machine.  It consists of three aluminum blocks...looks to
> be machined from 1 10mm x 8 mm block (8$ for 6 ft on McMasterCarr)

Yeah - claiming a $10 solution that involves three custom milled
aluminum blocks doesn't seem quite fair. Most DIYbio people won't have
access to those kinds of resources. Otherwise, I'm sure Tito &Co could
claim a much lower price as well, if they didn't count the cost for
their custom milled aluminum block, or the cost of laser cutting the
box, or manufacturing the circuit boards, or...

That being said - I'd love to see an estimate of how much this design
would cost in kit form - including commercially milled aluminum
blocks, and everything needed for temperature calibration. Or perhaps
the estimated cost per PCR reaction (including amortized equipment and
any labor costs), if you can only run one reaction at a time, and need
to switch out the tubing each time.

Jonathan Cline

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Sep 14, 2011, 4:06:54 PM9/14/11
to DIYbio, jcline
On Sep 14, 12:23 pm, Jonathan Cline <jncl...@gmail.com> wrote:
> On Sep 14, 9:46 am, Simon Quellen Field <sfi...@scitoys.com> wrote:
>
> > PCR experts -- how critical are the temperatures, and why?
>
> I am not a PCR expert however feedback I've received is that
> accuracy of +/- 2 degrees C is OK in most cases.


In fact what comes to mind is if water quality might be more
important for the DIYer than the temperature accuracy of the
thermocycler. I doubt any DIYers will be using sterile
water, probably just using distilled from the grocery store.
Although, DIYers may not notice the error anyway.

Reference:
http://www.millipore.com/lab_water/clw4/pcr

Mac Cowell

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Sep 16, 2011, 4:05:14 PM9/16/11
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Dasani water is reverse-osmosis purified. Trace amounts of various nutritional minerals are added after the fact. Would be interesting to figure out if they matter for PCR or electrophoresis.

231.313.9062 // @100ideas // sent from my rotary phone

John Griessen

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Sep 16, 2011, 5:29:34 PM9/16/11
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On 09/16/2011 03:05 PM, Mac Cowell wrote:
> Dasani water is reverse-osmosis purified. Trace amounts of various nutritional minerals are added after the fact.
Would be interesting to figure out if they matter for PCR or electrophoresis.

>> On Sep 14, 12:23 pm, Jonathan Cline<jncl...@gmail.com> wrote:
>>
>> In fact what comes to mind is if water quality might be more
>> important for the DIYer than the temperature accuracy of the
>> thermocycler.

I've heard before that the purity requirement for soda pop was more stringent than any natural water.
Wouldn't it be funny if Dasani water (by Coca Cola) and some added drops of Gatorade was just right
for electrophoresis resistance adjusting.

Cathal Garvey

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Sep 16, 2011, 6:32:08 PM9/16/11
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What a disgustingly wasteful way to make drinking water! Ow. Now I know to avoid that if I'm ever unlucky enough to need bottled water over yonder.

When it comes to ions and DNA, Ca, Mg and Mn spring to mind as most relevant catalytic ions, but that's top of the head stuff. Others will of course play roles with specific enzymes, like cobalt.

Adding cheating agents such as citrate or edta will sequester compatible ions one-for-one, so dose by molarity not weight.

Nathan McCorkle

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Sep 19, 2011, 9:41:18 AM9/19/11
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so my roommate just bought a laser cutter, and we have a makerbot...
once we finish aligning the optics, I'm sure he'd love if I did some
prototyping for a PCR machine.

I'm interested in seeing sketches of how a hot-air based cycler would
look. What I really mean is how the intake and exhaust manifolds would
look, because I think they should promote even flow (at least on a
short term average) amongst all the sample tubes.

Maybe we could directly use the OpenPCR firmware, modified to switch a
heater instead of a peltier.

--

John Griessen

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Sep 19, 2011, 11:50:25 AM9/19/11
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On 09/19/2011 08:41 AM, Nathan McCorkle wrote:
> I'm interested in seeing sketches of how a hot-air based cycler would
> look. What I really mean is how the intake and exhaust manifolds would
> look, because I think they should promote even flow (at least on a
> short term average) amongst all the sample tubes.

Here's a rough sketch of a temp controlled chamber for a carousel holding
vials to spin in.

http://ecosensory.com/diybio/thermo-cycler-carousel-air-flow-1.gif

The turbulence of spinning at least 2 revs per second (120RPM)
along with minimal solid contact with vials will keep all vials the same
as far as heat exchange.

Here's a diagram of an easy to fabricate tube well shape that minimizes
contact with the vials:

http://ecosensory.com/diybio/carousel_tube_wells-1.jpg

Controlling the doors with continuous position might not be
possible, but snapping them open and shut often seems easy.
Steady state would not require doors to move much, just when
changing/ramping temperatures -- so they would not wear out.
The material I am thinking of for doors is a flexible
plastic composite with piezo effects. I've not tried this yet,
and not sure of stiffness of the material, so the doors that
stick out in the air flow might not work that way if the material
is too flimsy. Some design around that will work though --
that piezo material can be used to make a fan.

Nathan McCorkle

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Sep 19, 2011, 12:12:00 PM9/19/11
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On Mon, Sep 19, 2011 at 11:50 AM, John Griessen <jo...@industromatic.com> wrote:
> On 09/19/2011 08:41 AM, Nathan McCorkle wrote:
>>
>> I'm interested in seeing sketches of how a hot-air based cycler would
>> look. What I really mean is how the intake and exhaust manifolds would
>> look, because I think they should promote even flow (at least on a
>> short term average) amongst all the sample tubes.
>
> Here's a rough sketch of a temp controlled chamber for a carousel holding
> vials to spin in.

spinning the tubes to equalize temps makes sense

>
> http://ecosensory.com/diybio/thermo-cycler-carousel-air-flow-1.gif
>
> The turbulence of spinning at least 2 revs per second (120RPM)
> along with minimal solid contact with vials will keep all vials the same
> as far as heat exchange.
>
> Here's a diagram of an easy to fabricate tube well shape that minimizes
> contact with the vials:
>
> http://ecosensory.com/diybio/carousel_tube_wells-1.jpg
>

pretty rough sketch, is the center the tube holder, or the 6 holes
around the center for the tubes?

> Controlling the doors with continuous position might not be
> possible, but snapping them open and shut often seems easy.
> Steady state would not require doors to move much, just when
> changing/ramping temperatures -- so they would not wear out.
> The material I am thinking of for doors is a flexible
> plastic composite with piezo effects.  I've not tried this yet,
> and not sure of stiffness of the material, so the doors that
> stick out in the air flow might not work that way if the material
> is too flimsy.  Some design around that will work though --
> that piezo material can be used to make a fan.
>

doors for what? I was imagining PWMing the heater to change temps,
since room temp is way out of the range for cycling. Unless you mean
to add room temp air to get the temp close to the set-point, then turn
the heater on to maintain the set point (can't just cool it down then
heat it back up, needs to hold at a temp for some time)

Also if there were multiple fans, one for fresh air, one for heated, I
don't see the need for a door, just that one of the fans would always
be on, maintaining positive pressure.

Thomas Stowe

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Sep 19, 2011, 12:20:07 PM9/19/11
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You might do some research on the Texas A&M PCR project that produced a PCR design awhile ago that was able to be made cheaply. I've seen schematics for it around. I remember it was somewhat hard for me to find. I'd look now, but I'm at work. G'luck.


Thomas C. Stowe
Texas Computer Services http://www.txpcservices.com
Portfolio/VCard/Resume/Blog http://www.thomasstowe.info


John Griessen

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Sep 19, 2011, 12:23:57 PM9/19/11
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On 09/19/2011 11:12 AM, Nathan McCorkle wrote:

> pretty rough sketch, is the center the tube holder, or the 6 holes
> around the center for the tubes?

center is tube carousel holder

> doors for what?
Doors change flow through hot zone or to ambient==cooler.

I was imagining PWMing the heater to change temps,

Sure that too, but take away the slowness of thermal masses changing temps
and just throw doors to get different temp and ramp the other way.

>
> Also if there were multiple fans,

Carousel is the fan. Simplicity.

JG

Nathan McCorkle

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Sep 19, 2011, 12:29:21 PM9/19/11
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hmm, really? OK, I'll look for some turbine 3D design files online,
maybe thingiverse has something.

>
> JG

John Griessen

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Sep 19, 2011, 12:54:52 PM9/19/11
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On 09/19/2011 11:29 AM, Nathan McCorkle wrote:
> hmm, really? OK, I'll look for some turbine 3D design files online,
> maybe thingiverse has something.

It does not need a turbine shape. It will be a functional fan with or without
vials set in place. If some vials missing, the holes will have plenty of air drag
to pull air along as it spins.

This design is something that can be mostly laser cut from sheet plastic
for easy manufacturing and low costs. The housing can be made on a rep-rap
or makerbot. This sketch is about holding cylindrical vials that have caps
that are wider with no ability to deal with plates, but future
possibility to work as an incubator
and liquid handler and transmission densitometer with many of the same parts.

John

Nathan McCorkle

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Sep 19, 2011, 1:05:29 PM9/19/11
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On Mon, Sep 19, 2011 at 12:54 PM, John Griessen <jo...@industromatic.com> wrote:
> On 09/19/2011 11:29 AM, Nathan McCorkle wrote:
>>
>> hmm, really? OK, I'll look for some turbine 3D design files online,
>> maybe thingiverse has something.
>
> It does not need a turbine shape.  It will be a functional fan with or
> without
> vials set in place.  If some vials missing, the holes will have plenty of
> air drag
> to pull air along as it spins.

how would you direct which way the air will flow, without turbine
features? I.e. what if the air gets pushed from in the cycler past the
heater, to the outside (heating the room, rather than the tubes)

also, 2 RPMs seems too slow, but I wouldn't want to depend on faster
speeds because it could cause chemical or protein gradients in the
tube (mayyyybbeeeee, I have no idea how fast it would have to spin for
this to happen)


>
> This design is something that can be mostly laser cut from sheet plastic
> for easy manufacturing and low costs.  The housing can be made on a rep-rap
> or makerbot.  This sketch is about holding cylindrical vials that have caps
> that are wider with no ability to deal with plates, but future
> possibility to work as an incubator
> and liquid handler and transmission densitometer with many of the same
> parts.
>
> John
>

John Griessen

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Sep 19, 2011, 1:17:27 PM9/19/11
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On 09/19/2011 12:05 PM, Nathan McCorkle wrote:
what if the air gets pushed from in the cycler past the
> heater, to the outside (heating the room, rather than the tubes)

The doors control that. Sure, it's just a theory at the moment.
I'll be testing it out though...

>
> also, 2 RPMs seems too slow, b

2 revs per second is a good low G-force speed.

John Griessen

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Sep 19, 2011, 1:31:00 PM9/19/11
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On 09/19/2011 12:05 PM, Nathan McCorkle wrote:
> how would you direct which way the air will flow, without turbine
> features?

Like an impeller pump, and by opening and closing ports (doors):


http://ecosensory.com/diybio/thermo-cycler-carousel-air-flow-2.gif

Nathan McCorkle

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Sep 19, 2011, 4:34:22 PM9/19/11
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Ok here are some designs to begin with....

The straight vanes look innefficient, is that so?
http://www.thingiverse.com/thing:7350

This looks better:
http://www.thingiverse.com/thing:6095

Thomas Stowe

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Sep 19, 2011, 4:50:04 PM9/19/11
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a neat way to power these types of fans is dremel tools. cheap as all hell too, especially when second-hand. controllers can be rigged if need be. of course, a diy fan circuit and motor from scavenged parts might be cheaper.


Thomas C. Stowe
Texas Computer Services http://www.txpcservices.com
Portfolio/VCard/Resume/Blog http://www.thomasstowe.info





John Griessen

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Sep 19, 2011, 6:29:45 PM9/19/11
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On 09/19/2011 03:34 PM, Nathan McCorkle wrote:

> The straight vanes look innefficient, is that so?
> http://www.thingiverse.com/thing:7350

We want low flow, low noise, and don't need it piped into a tube.

Having the carousel for vials be the impeller is more efficient.
When your goal is to exchange heat with the vials on the carousel,
and you do not care about directing flow in a tube. All the flow we
need is turbulent mostly to even out temperatures, and enough to
exchange heat, which is easy and doesn't need any optimizing or
calculations even. Pumps can be optimized, but we don't need a pump,
we just need heat flow.

JG

Nathan McCorkle

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Sep 19, 2011, 7:06:50 PM9/19/11
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I don't follow 'not needing a pump/fan', how will air surrounding a
hot coil be directed past tubes needing heat? There needs to be a fan,
in my opinion the vanes should look like a helical gear, to draw air
past the upward and past the tubes. If the carousel is only to even
out the temps, then a fan behind the coil would be needed to push any
air through the system.

> JG

Thomas Stowe

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Sep 19, 2011, 7:42:51 PM9/19/11
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actually, some of the PCR designs that i've seen really didn't rely on much beyond the fact that part of the tube was covered and part wasn't. that did enough to get the job done. i'm sure that both would work, but adding a bunch of equipment not stricly needed might not be the way to go. i guess it depends on what goal you're trying to achieve.

housing it inside a computer case, like the OpenPCR, sure...


I think that what you're missing is that PCRs often rely upon reactor geometry to achieve what you think needs to be done by a fan or pump.

Here, this will help you understand (and she's got a damned sexy voice anyway so worth listening to).

Rapid PCR Thermocycling using Microscale Thermal Convection


It's probably the best instructional video on the subject matter that I've seen.


Thomas C. Stowe
Texas Computer Services http://www.txpcservices.com
Portfolio/VCard/Resume/Blog http://www.thomasstowe.info





Nathan McCorkle

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Sep 19, 2011, 7:58:13 PM9/19/11
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On Mon, Sep 19, 2011 at 7:42 PM, Thomas Stowe <stowe....@gmail.com> wrote:
> actually, some of the PCR designs that i've seen really didn't rely on much
> beyond the fact that part of the tube was covered and part wasn't. that did

sure for things like lightbulb PCR, but my understanding of what John
and I have been talking about is akin to pointing a hair blow dryer
towards and then away from the PCR tubes.

> enough to get the job done. i'm sure that both would work, but adding a
> bunch of equipment not stricly needed might not be the way to go. i guess it
> depends on what goal you're trying to achieve.

an extra 100mm computer fan isn't 'a bunch' of stuff though, its about
$4 new (if that)

> housing it inside a computer case, like the OpenPCR, sure...
> http://openpcr.org/build-it/

openPCR isn't housed in a computer case, its in laser-cut luan.

> I think that what you're missing is that PCRs often rely upon reactor
> geometry to achieve what you think needs to be done by a fan or pump.

hmm, that seems to rely more heavily on thermal physics and
engineering... not my idea of a first iteration at a new type of PCR
cycler

> Here, this will help you understand (and she's got a damned sexy voice
> anyway so worth listening to).
>
> Rapid PCR Thermocycling using Microscale Thermal Convection
>
> http://www.jove.com/details.php?id=2366
> It's probably the best instructional video on the subject matter that I've
> seen.
>

Thanks, I'll check it out

John Griessen

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Sep 19, 2011, 10:20:06 PM9/19/11
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On 09/19/2011 06:06 PM, Nathan McCorkle wrote:
> I don't follow 'not needing a pump/fan', how will air surrounding a
> hot coil be directed past tubes needing heat?

by opening or shutting doors at which there is a pressure difference
from fan action and flow will happen as soon as doors open.

There needs to be a fan,

There is a fan. The carousel *is* a fan impeller in a housing as I've sketched
in prev. emails.

> in my opinion the vanes should look like a helical gear, to draw air
> past the upward and past the tubes.

OK, but with a separate turbine is a different design without
much reuse of parts and I don't see why it's necessary -- or how it could
be made for a profit as open hardware.

The sketches tell a lot. Can't answer much more for a couple of days.
Busy with a concrete pour Tues.

JG

Nathan McCorkle

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Sep 19, 2011, 10:44:14 PM9/19/11
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On Mon, Sep 19, 2011 at 10:20 PM, John Griessen <jo...@industromatic.com> wrote:
> On 09/19/2011 06:06 PM, Nathan McCorkle wrote:
>>
>> I don't follow 'not needing a pump/fan', how will air surrounding a
>> hot coil be directed past tubes needing heat?
>
> by opening or shutting doors at which there is a pressure difference
> from fan action and flow will happen as soon as doors open.
>

I guess I'm just thinking that air wouldn't circulate through the
heater duct without the vanes/blades of the fan (which happens to be
the carousel) being directional. The non-helical fan I mentioned from
thingiverse looks like a boat paddlewheel, doesn't seem non-directed
air flow is the best way to get high ramp rates.

> There needs to be a fan,
>
> There is a fan.  The carousel *is* a fan impeller in a housing as I've
> sketched
> in prev. emails.

How fast would it have to spin to generate sufficient air mass and
heat transfer though? I don't think 2 RPMs are going to cut it.

>
>> in my opinion the vanes should look like a helical gear, to draw air
>> past the upward and past the tubes.
>
> OK, but with a separate turbine is a different design without
> much reuse of parts and I don't see why it's necessary -- or how it could
> be made for a profit as open hardware.

one fan versus two is not a profit killer, I'm not sure how you see
that, but I wasn't saying its necessary, but if you want to spin at 2
RPM to even out temp eddies, then yeah I think another fan to actually
blow air around is needed.


>
> The sketches tell a lot.  Can't answer much more for a couple of days.
> Busy with a concrete pour Tues.
>
> JG
>

John Griessen

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Sep 19, 2011, 11:05:52 PM9/19/11
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On 09/19/2011 09:44 PM, Nathan McCorkle wrote:
> if you want to spin at 2
> RPM
Not 2 RPM 2 rev / sec. 120RPM.

John Griessen

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Sep 19, 2011, 11:14:59 PM9/19/11
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The main question in a thermocycler is what container do you want to thermal cycle?
I am assuming a flip capped vial. Is that right on?
What container?

Then the next steps are
1. make prototype stuff
2. test prototype stuff
3. repeat til working as few times as possible based on hunches and experience and inductive logic.

No heat flow calcs. Takes too long. The container is one of the worst heat flow
gaps being plastic. Heater behind a door is a no brainer for super rapid air temp change
copied from GM cars. There will be no problem of transferring heat at all. The hot door
will have to be shut 2 seconds after the start of a ramp up is my bet. And during the ramp it
will open and shut every 3/4 second likely. That will all be part of a heuristic
semi-PID control with a little nonlinear/nonintegral preboost and it will tune up easily.
Next comes building parts, testing parts.

JG

Thomas Stowe

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Sep 19, 2011, 11:54:48 PM9/19/11
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Heat calcs can be done quite easily in fact.
DIY doesn't mean "ghetto" solutions. I mean, building a device like a PCR doesn't mean it will have to have 20 iterations of the same hardware to get results. Tools like Spotfire, S-Plus, Matlab and more all have free trials. It's not going to cost you an arm and a leg to do some modeling beforehand and in fact, most people you ask will tell you that you'd be wasting your time not to.

Hell, you can probably find a free version of a text similar to http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html as well as a tutorial for setting up the PCR thermodynamic calculations. If you're building equipment like this and PDE is too much for you, you really might consider spending more time learning. It's not just cobble together, add dna and Pfu based upon general design and go if you're creating something that'll either be respectable or be able to be used as a template for a great number of people. Being creative and thinking outside of the box is fine, that's how great developments are made. But don't mistake "I need to be getting things done" for the fact that something is boring or tedious when it'll save you time, energy and in all feasible likelihood give you better results if you spend the time doing it.

Other PCR docs for those interested:




Thomas C. Stowe
Texas Computer Services http://www.txpcservices.com
Portfolio/VCard/Resume/Blog http://www.thomasstowe.info









JG

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Patrik

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Sep 20, 2011, 3:02:01 AM9/20/11
to DIYbio
On Sep 16, 3:32 pm, Cathal Garvey <cathalgar...@gmail.com> wrote:
>
> Adding cheating agents such as citrate or edta will sequester compatible
> ions one-for-one, so dose by molarity not weight.

Cheating agents? Oh, I think we want to use as many cheating agents as
we can get away with ;-)

Cathal Garvey

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Sep 20, 2011, 3:14:54 AM9/20/11
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"CyclerCan" was air-based. Got air gun plus cooler fan.

John Griessen

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Sep 20, 2011, 4:31:52 AM9/20/11
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On 09/19/2011 10:54 PM, Thomas Stowe wrote:
> Heat calcs can be done quite easily in fact.
Sure, but modeling what? About all I plan is the series chain of thermal resistances
of plastic container, heat exchange air, thermal mass of chamber walls, heater.
And then only to get some rough starting points for a control system. Using the system
will be the best chooser of settings.

The heater and chamber thermal mass and convection air is such a loosely connected system
I doubt a simulation would be helpful as first step. Especially when you know you can just dump some
heat energy and most of it will stay in the machine for a couple of minutes...then just
control away by varying door openings while hot zone is open and cooling off, or shut and
steady state with little heat input.


have to have 20 iterations of the
> same hardware to get results.

20? No, 3 iterations of 1/2 of the design are normal for design of anything good.
And half is good the first try usually.
.
.
.


If you're building equipment like this and PDE is too much
> for you, you really might consider spending more time learning.

I'm just fine at partials and time domain calcs, thanks for sharing, but will
you be volunteering any effort on this?

John

Zebedeeboy

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Sep 21, 2011, 1:20:28 PM9/21/11
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I'm not sure you would need to bother with doors to direct the air flow. If the airflow past the element is high enough the changes in air temp should be pretty fast. The all you would need is a decent temp sensor to switch the coil on/off. I don't think anyone has mentiones it yet but Corbett solved this particular problem a while ago with the RotorGene qPCR. I don't think it has any other moving parts other than the rotor/fan that carries the PCR tubes.

Zeb

Sent from Samsung Mobile



John Griessen <jo...@industromatic.com> wrote:


On 09/19/2011 06:06 PM, Nathan McCorkle wrote:
> I don't follow 'not needing a pump/fan', how will air surrounding a
> hot coil be directed past tubes needing heat?

by opening or shutting doors at which there is a pressure difference
from fan action and flow will happen as soon as doors open.

There needs to be a fan,

There is a fan.  The carousel *is* a fan impeller in a housing as I've sketched
in prev. emails.

> in my opinion the vanes should look like a helical gear, to draw air
> past the upward and past the tubes.

OK, but with a separate turbine is a different design without
much reuse of parts and I don't see why it's necessary -- or how it could
be made for a profit as open hardware.

The sketches tell a lot.  Can't answer much more for a couple of days.
Busy with a concrete pour Tues.

JG

John Griessen

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Sep 21, 2011, 1:56:48 PM9/21/11
to diy...@googlegroups.com
On 09/21/2011 12:20 PM, Zebedeeboy wrote:
> I'm not sure you would need to bother with doors to direct the air flow. If the airflow past the element is high enough the
> changes in air temp should be pretty fast. The all you would need is a decent temp sensor to switch the coil on/off.

If you keep the thermal mass of the heater very low that could work. I really like the doors for access to ambient air
so I don't need a TE cooler. Once you control some doors for ambient air, then using some for heat is a natural also.
I always have a design goal to perform to a quantitative level rather than "pretty fast". I'd like to offer programmable ramp
times of 1 deg C per second. Maybe the heater doors could be left off, but the ambient doors are going to be needed
to have any benefit of air heat exchange.

I don't think
> anyone has mentiones it yet but Corbett solved this particular problem a while ago with the RotorGene qPCR. I don't think it has
> any other moving parts other than the rotor/fan that carries the PCR tubes.

Dang! They have glitzy industrial designed packages around their equip and really brag about a carousel used to hold vials. That
means they may have patented it...hmmm...

number 6814934 and . 6,787,338; 7,238,321; 7,081,226; 6,174,670; 6,245,514; 6,569,627; 6,303,305;
6,503,720; 5,871,908; 6,691,041; 7,387,887; 7,273,749; 7,160,998; U.S. Patent Application Nos. 2003/0224434, and 2006-0019253, and
PCT Patent Application No. WO 2007/035806, and
all continuations and divisionals, and corresponding claims in patents and patent applications outside the United States, owned by
the University of Utah Research Foundation, Idaho Technology, Inc., Evotec
Biosystems GmbH, and/or Roche Diagnostics GmbH.

That's a lot to read. Will take a while...

JG

Nathan McCorkle

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Sep 25, 2011, 10:36:17 PM9/25/11
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Didn't read any of it yet.

Do you think luan (the thin plywood) would be OK for a prototype?

> JG
>
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John Griessen

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Sep 26, 2011, 9:57:01 AM9/26/11
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On 09/25/2011 09:36 PM, Nathan McCorkle wrote:
> Do you think luan (the thin plywood) would be OK for a prototype?

Sure, why not? I bet you're thinking of laser cuttables, right?
Get your smoke exhaust vent going and tell us about it!
You can make 3D shapes by stacking layers that are glued together
of anything...

Try using HeeksCAD for the 3D and I will be able to help with ideas
and versions. Plus anyone else since it is free OSS. And it's good!
It has parameterized 2D sketches and python scripting.

JG

Nathan McCorkle

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Sep 26, 2011, 10:32:02 AM9/26/11
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Yep thinkin laser cut pieces... Ideas for easy to source heaters... Would like to avoid using a power FET for now, if possible.

Will also need to think about what to use to actuate the doors, cheap and quick linear actuator, but from where/what?

Thomas Stowe

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Sep 26, 2011, 10:58:47 AM9/26/11
to diy...@googlegroups.com
what about those cheap heating fans from walmart that sell for $20 a pair or (I think I've seen this second item related to PCRs before) the thermoregulators for aquariums?


Thomas C. Stowe
Texas Computer Services http://www.txpcservices.com
Portfolio/VCard/Resume/Blog http://www.thomasstowe.info